9f6ac938b7
* Update and fix bcftools package This PR updates bcftools to 1.10.2 and is dependent on PR #14504. This PR also fixes builds of other versions. Versions 1.2-1.4 did not use autotools so when the packaeg was converted to use autotools with version 1.6 those older versions could no longer build. Also, those versions needed to be patched to use an external htsllib. The method of finding the external htslib is also different for those older versions. In addition, this PR adds two variants to bcftools: - libgsl - perl-filters Finally, dependencies for perl and python are added, and an unused dependency for libzip was removed. * Do not use '@' in variant description The '@' character in a variant description will cause a problem with `spack info`. ``` ==> Error: Incomplete color format: '@' in expressions, for @1.8: ``` * Fix error with python2 processing this package
110 lines
6.0 KiB
Diff
110 lines
6.0 KiB
Diff
--- a/Makefile 2015-02-03 10:27:19.000000000 -0600
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+++ b/Makefile 2020-01-13 21:22:54.554904229 -0600
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@@ -30,10 +30,11 @@
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# Adjust $(HTSDIR) to point to your top-level htslib directory
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HTSDIR = htslib-1.2.1
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-include $(HTSDIR)/htslib.mk
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-HTSLIB = $(HTSDIR)/libhts.a
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-BGZIP = $(HTSDIR)/bgzip
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-TABIX = $(HTSDIR)/tabix
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+#include $(HTSDIR)/htslib.mk
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+HTSINC = $(HTSDIR)/include
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+HTSLIB = -L$(HTSDIR)/lib -lhts
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+BGZIP = $(HTSDIR)/bin/bgzip
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+TABIX = $(HTSDIR)/bin/tabix
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CC = gcc
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CFLAGS = -g -Wall -Wc++-compat -O2
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@@ -44,7 +45,7 @@
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vcfcall.o mcall.o vcmp.o gvcf.o reheader.o convert.o vcfconvert.o tsv2vcf.o \
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vcfcnv.o HMM.o vcfplugin.o consensus.o ploidy.o version.o \
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ccall.o em.o prob1.o kmin.o # the original samtools calling
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-INCLUDES = -I. -I$(HTSDIR)
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+INCLUDES = -I. -I$(HTSINC)
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# The polysomy command is not compiled by default because it brings dependency
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# on libgsl. The command can be compiled wth `make USE_GPL=1`. See the INSTALL
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@@ -52,7 +53,7 @@
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ifdef USE_GPL
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CFLAGS += -DUSE_GPL
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OBJS += polysomy.o
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- LDLIBS = -lgsl -lcblas
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+ LDLIBS = -lgsl -lgslcblas
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endif
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prefix = /usr/local
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@@ -102,8 +103,8 @@
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PLUGINS = $(PLUGINC:.c=.so)
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PLUGINM = $(PLUGINC:.c=.mk)
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-%.so: %.c version.h version.c $(HTSDIR)/libhts.so
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- $(CC) $(CFLAGS) $(INCLUDES) -fPIC -shared -o $@ version.c $< -L$(HTSDIR) -lhts
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+%.so: %.c version.h version.c
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+ $(CC) $(CFLAGS) $(INCLUDES) -fPIC -shared -o $@ version.c $< $(HTSLIB)
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-include $(PLUGINM)
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@@ -116,20 +117,20 @@
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tsv2vcf_h = tsv2vcf.h $(htslib_vcf_h)
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filter_h = filter.h $(htslib_vcf_h)
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prob1_h = prob1.h $(htslib_vcf_h) $(call_h)
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-roh_h = HMM.h $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(HTSDIR)/htslib/kstring.h $(HTSDIR)/htslib/kseq.h $(bcftools_h)
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+roh_h = HMM.h $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(HTSINC)/htslib/kstring.h $(HTSINC)/htslib/kseq.h $(bcftools_h)
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cnv_h = HMM.h $(htslib_vcf_h) $(htslib_synced_bcf_reader_h)
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main.o: main.c $(htslib_hts_h) version.h $(bcftools_h)
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-vcfannotate.o: vcfannotate.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(HTSDIR)/htslib/kseq.h $(bcftools_h) vcmp.h $(filter_h)
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-vcfplugin.o: vcfplugin.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(HTSDIR)/htslib/kseq.h $(bcftools_h) vcmp.h $(filter_h)
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-vcfcall.o: vcfcall.c $(htslib_vcf_h) $(HTSDIR)/htslib/kfunc.h $(htslib_synced_bcf_reader_h) $(bcftools_h) $(call_h) $(prob1_h)
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-vcfconcat.o: vcfconcat.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(HTSDIR)/htslib/kseq.h $(bcftools_h)
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+vcfannotate.o: vcfannotate.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(HTSINC)/htslib/kseq.h $(bcftools_h) vcmp.h $(filter_h)
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+vcfplugin.o: vcfplugin.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(HTSINC)/htslib/kseq.h $(bcftools_h) vcmp.h $(filter_h)
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+vcfcall.o: vcfcall.c $(htslib_vcf_h) $(HTSINC)/htslib/kfunc.h $(htslib_synced_bcf_reader_h) $(bcftools_h) $(call_h) $(prob1_h)
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+vcfconcat.o: vcfconcat.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(HTSINC)/htslib/kseq.h $(bcftools_h)
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vcfconvert.o: vcfconvert.c $(htslib_vcf_h) $(htslib_bgzf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) $(filter_h) $(convert_h) $(tsv2vcf_h)
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vcffilter.o: vcffilter.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) $(filter_h) rbuf.h
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vcfgtcheck.o: vcfgtcheck.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h)
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vcfindex.o: vcfindex.c $(htslib_vcf_h) $(htslib_tbx_h)
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vcfisec.o: vcfisec.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) $(filter_h)
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-vcfmerge.o: vcfmerge.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) vcmp.h $(HTSDIR)/htslib/khash.h
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+vcfmerge.o: vcfmerge.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) vcmp.h $(HTSINC)/htslib/khash.h
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vcfnorm.o: vcfnorm.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_faidx_h) $(bcftools_h) rbuf.h
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vcfquery.o: vcfquery.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) $(filter_h) $(convert_h)
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vcfroh.o: vcfroh.c $(roh_h)
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@@ -137,20 +138,20 @@
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vcfsom.o: vcfsom.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h)
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vcfstats.o: vcfstats.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(htslib_faidx_h) $(bcftools_h)
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vcfview.o: vcfview.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) $(filter_h)
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-reheader.o: reheader.c $(htslib_vcf_h) $(htslib_bgzf_h) $(HTSDIR)/htslib/kseq.h $(bcftools_h)
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+reheader.o: reheader.c $(htslib_vcf_h) $(htslib_bgzf_h) $(HTSINC)/htslib/kseq.h $(bcftools_h)
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tabix.o: tabix.c $(htslib_bgzf_h) $(htslib_tbx_h)
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-ccall.o: ccall.c $(HTSDIR)/htslib/kfunc.h $(call_h) kmin.h $(prob1_h)
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+ccall.o: ccall.c $(HTSINC)/htslib/kfunc.h $(call_h) kmin.h $(prob1_h)
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convert.o: convert.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) $(convert_h)
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tsv2vcf.o: tsv2vcf.c $(tsv2vcf_h)
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em.o: em.c $(htslib_vcf_h) kmin.h $(call_h)
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-filter.o: filter.c $(HTSDIR)/htslib/khash_str2int.h $(filter_h) $(bcftools_h) $(htslib_hts_defs_h) $(htslib_vcfutils_h)
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+filter.o: filter.c $(HTSINC)/htslib/khash_str2int.h $(filter_h) $(bcftools_h) $(htslib_hts_defs_h) $(htslib_vcfutils_h)
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gvcf.o: gvcf.c $(call_h)
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kmin.o: kmin.c kmin.h
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-mcall.o: mcall.c $(HTSDIR)/htslib/kfunc.h $(call_h)
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+mcall.o: mcall.c $(HTSINC)/htslib/kfunc.h $(call_h)
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prob1.o: prob1.c $(prob1_h)
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vcmp.o: vcmp.c $(htslib_hts_h) vcmp.h
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polysomy.o: polysomy.c $(htslib_hts_h)
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-consensus.o: consensus.c $(htslib_hts_h) $(HTSDIR)/htslib/kseq.h rbuf.h $(bcftools_h) $(HTSDIR)/htslib/regidx.h
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+consensus.o: consensus.c $(htslib_hts_h) $(HTSINC)/htslib/kseq.h rbuf.h $(bcftools_h) $(HTSINC)/htslib/regidx.h
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version.o: version.h version.c
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test/test-rbuf.o: test/test-rbuf.c rbuf.h
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@@ -158,7 +159,7 @@
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test/test-rbuf: test/test-rbuf.o
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$(CC) $(CFLAGS) -o $@ -lm -ldl $<
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-bcftools: $(HTSLIB) $(OBJS)
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+bcftools: $(OBJS)
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$(CC) $(CFLAGS) -o $@ $(OBJS) $(HTSLIB) -lpthread -lz -lm -ldl $(LDLIBS)
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doc/bcftools.1: doc/bcftools.txt
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